I'm speaking from advice given to me when I got my first Yorkie and from personal experience. 9 wks is too young to have free roam of an entire house. She will keep pooping everywhere until you confine her at least to one room. I had the pen also. They will learn to pee/poop on the pad in their pen. But if you let them loose it is difficult for them to run all the way back to that pee pad . Unless you put pee pads everywhere which doesnt look pretty and doesnt always work. I had my hubby make a gate to my family room so he was confined to the familyroom only and he soon learned to use 1 pee pad in the familyroom. They will have accidents now and then. He is now almost 2yrs old and does pretty well. We ended up removing all the rug except the bedroom rug. He now roams free in the house, we keep the bedroom doors closed and he does use a pee pad when in my bedroom.
The only thing I could tell you is that it can take 3 months to train them ,1 yr and some are never fully trained ...only time will tell.BE PATIENT.It sounds easy I know but you dont want a pup that will pee out of nervousness either. I had one since she was 8 wks old and she always would pee when we tried to carry her or call her.My vet told me that they can be traumatized in the first weeks and never get over it
Genie